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Yorodumi- PDB-1wqh: Crystal structure of ribosome recycling factor from Mycobacterium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wqh | ||||||
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Title | Crystal structure of ribosome recycling factor from Mycobacterium tuberculosis | ||||||
Components | Ribosome recycling factor | ||||||
Keywords | TRANSLATION / Translation factor / triple-HELIX bundle / protein synthesis | ||||||
Function / homology | Function and homology information translation termination factor activity / ribosomal large subunit binding / translational termination / peptidoglycan-based cell wall / translation / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Saikrishnan, K. / Kalapala, S.K. / Varshney, U. / Vijayan, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: X-ray structural studies of Mycobacterium Tuberculosis RRF and a comparative study of RRFS of known structure. Molecular plasticity and biological implications Authors: Saikrishnan, K. / Kalapala, S.K. / Varshney, U. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Purification, crystallization and preliminary X-ray studies of Mycobacterium tuberculosis RRF Authors: Saikrishnan, K. / Kalapala, S.K. / Bidya Sagar, M. / Rao, A.R. / Varshney, U. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wqh.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wqh.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/1wqh ftp://data.pdbj.org/pub/pdb/validation_reports/wq/1wqh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20861.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P66734, UniProt: P9WGY1*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, cadmium acetate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 2003 |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 5581 / Num. obs: 5237 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.113 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.889 / SU B: 21.699 / SU ML: 0.405 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.883 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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